Deep exploration of microbial profiles
…BRIEF INTRO IN PROGRESS…
Snakemake workflow for exploratory data analysis
A tentative snakemake workflow that defines data exploration rules in a DAG (directed acyclic graph) format. A detailed interactive snakemake HTML report is available here. Use a wider screen to get a better interactive snakemake report.
Citation
Please consider citing the iMAP article[1] if you find any part of the IMAP practical user guides helpful in your microbiome data analysis.
References
[1]
Buza, T. M., Tonui, T., Stomeo, F., Tiambo, C.,
Katani, R., Schilling, M., … Kapur, V. (2019). iMAP: An integrated
bioinformatics and visualization pipeline for microbiome data analysis.
BMC Bioinformatics, 20. https://doi.org/10.1186/S12859-019-2965-4
Appendix
Project main tree
.
├── LICENSE
├── README.md
├── config
│  ├── config.yml
│  ├── samples.tsv
│  └── units.tsv
├── css
├── dags
│  ├── rulegraph.png
│  └── rulegraph.svg
├── data
│  ├── feature_table.qza
│  ├── processed_data.rda
│  ├── processed_objects.rda
│  ├── rooted_tree.qza
│  ├── sample_metadata.tsv
│  ├── shannon_vector.qza
│  └── taxonomy.qza
├── figures
│  ├── q2r_barplot.png
│  ├── q2r_barplot.svg
│  ├── q2r_jitterplot.png
│  ├── q2r_jitterplot.svg
│  ├── q2r_lineplot.png
│  ├── q2r_pcoa.png
│  ├── q2r_venndiagram.png
│  └── q2r_venndiagram.svg
├── images
│  ├── bkgd.png
│  ├── coders.png
│  ├── ml.png
│  ├── smkreport
│  │  └── screenshot.png
│  └── vizcover.png
├── imap-data-visualization.Rproj
├── index.Rmd
├── library
│  ├── apa.csl
│  ├── export.bib
│  ├── imap.bib
│  ├── packages.bib
│  └── references.bib
├── report.html
├── results
│  └── project_tree.txt
├── styles.css
└── workflow
├── Snakefile
├── envs
│  └── environment.yml
├── report
│  ├── barplot.rst
│  ├── boxplots.rst
│  ├── hcluster.rst
│  ├── heatmap.rst
│  ├── jitterplot.rst
│  ├── lineplot.rst
│  ├── nmds.rst
│  ├── pcaordi.rst
│  ├── pcoa.rst
│  ├── scatter.rst
│  ├── venndiagram.rst
│  ├── volcano.rst
│  └── workflow.rst
├── rules
│  ├── import_demo_data.smk
│  ├── render_index.smk
│  ├── rmd_report.smk
│  ├── rules_dag.smk
│  ├── visual_types.smk
│  └── visuals.smk
└── scripts
├── README.md
├── alpha.R
├── barplot.R
├── build_bs4_book.bash
├── common.R
├── custom_theme.R
├── heatmap.R
├── import_demo_data.R
├── jitterplot.R
├── lefse.R
├── lineplot.R
├── load_processed_objects.R
├── part4.R
├── pcoa.R
├── qiime2R.R
├── qiime2csv.R
├── rarefy.R
├── read_matrix.R
├── render.R
├── rules_dag.sh
├── smk_html_report.sh
├── tree.sh
├── venndiagram.R
└── volcanoplot.R
14 directories, 82 files
Troubleshooting of FAQs
- Question
- Question
-
Answer
-
Answer